Andreas R. Pfenning

A molecular and spinal circuit basis for the functional segregation of itch and pain

The paper identifies functionally distinct subtypes within Grpr+ neurons in the dorsal horn that mediate itch and mechanical allodynia, demonstrating the utility of genomic enhancer-based strategies for modality-specific targeting.

An Epigenetic Signature of Vulnerable Neurons is Under Selective Pressure Associated with Longevity Across Placental Mammals.

The paper identifies cell-type-specific epigenetic signatures linked to neuronal vulnerability and longevity across placental mammals using epigenomics and AI.

Conditional polygenic enrichment distinguishes causal from tagging disease-critical cell populations in single-cell RNA-seq

This paper introduces scDRS-FM, a method to distinguish causal from tagging disease associations in scRNA-seq data, showing it improves power and accuracy in identifying disease-relevant cell populations.

Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics

The paper introduces CTACIT to fine-map neuropsychiatric regulatory variants by integrating conservation scores with cell type-specific open chromatin data across species.

RERconverge Update: Runtime Reduction and Analysis Function Overhaul

The paper updates the RERconverge package with faster algorithms and new analysis features for studying convergent evolution at the genomic level.

Local control of dopamine release in nucleus accumbens gates opioid withdrawal aversion

The paper identifies Tshz1 neurons in the nucleus accumbens as critical for withdrawal aversion by modulating dopamine release and mGluR8 activity, offering a new therapeutic target for opioid use disorder.

Challenges in predicting chromatin accessibility differences between species

This study trains CNNs to predict chromatin accessibility across species but finds poor performance in predicting quantitative differences between species.

A consensus spinal cord cell type atlas across mouse, macaque, and human

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum

The paper builds a multimodal atlas of medium spiny neurons in the primate striatum, identifying new subtypes and linking them to disease associations.

Context-dependent regulatory variants in Alzheimer's disease

The paper identifies context-dependent regulatory variants in Alzheimer's disease by analyzing their effects across different cellular contexts using MPRAs and machine learning.

Etiological basis for chronic pain genetic variation in brain and dorsal root ganglia cell types

This paper identifies cell-type-specific genetic variants associated with chronic pain using GWAS and scRNA-seq data from brain and dorsal root ganglia tissues.

Combining Machine Learning and Multiplexed, In Situ Profiling to Engineer Cell Type and Behavioral Specificity

The paper develops a platform combining machine learning and multiplexed in situ screening to identify enhancers with cell-type and behavioral specificity for neural circuit engineering.

Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex.

The paper identifies cell type-specific enhancers for the DLPFC in NHPs using single nucleus RNA-Seq and ATAC-Seq, validates them with AAV injections, and demonstrates functional expression in specific neuron types.

An in vivo massively parallel platform for deciphering tissue-specific regulatory function

The paper introduces WhAMPRA, an in vivo MPRA platform in mice, to assess tissue-specific regulatory functions of genetic variants and enhancers.

Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph

KGWAS improves GWAS power in small cohorts by integrating a functional knowledge graph, discovering more associations for rare diseases.

Spatial, transcriptomic and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition

The paper links chronic pain genetic variants to dorsal horn neuron subtypes using multi-species single-cell and spatial transcriptomic analyses.

RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution

The paper expands RERconverge to analyze multi-categorical traits by introducing methods for ancestral state reconstruction, statistical tests, and phylogenetic permutations, showing improved performance in identifying diet-related genes and pathways.

Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease

The paper uses CNN regression models to predict the impact of AD-associated variants on open chromatin in different cell types, finding greater effects in peripheral cells than in microglia or neurons.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

Single nuclei transcriptomics in human and non-human primate striatum implicates neuronal DNA damage and proinflammatory signaling in opioid use disorder

The paper uses single nuclei RNA-sequencing to identify striatal cell types in humans and rhesus macaques and finds molecular changes linked to opioid use disorder.

Integrative multi-dimensional characterization of striatal projection neuron heterogeneity in adult brain

The paper characterizes striatal projection neuron heterogeneity in mice using single-nuclei multi-omics and spatial mapping, revealing distinct subtypes with unique receptor expression and disease risk contributions.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Cell type-specific histone acetylation profiling of Alzheimer's Disease subjects and integration with genetics

The paper profiles H3K27ac in brain cell types from AD patients and finds acetylation differences in oligodendrocytes linked to AD risk genes and pathways.

Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.

The paper identifies that DNA double strand breaks in neurons activate immune pathways, leading to microglia activation in neurodegeneration.

Convergent gene expression highlights shared vocal motor microcircuitry in songbirds and humans

The paper identifies convergent gene expression patterns between songbird and human vocal motor circuits, highlighting shared molecular specializations in specific brain regions.